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    SLC66A1 solute carrier family 66 member 1 [ Homo sapiens (human) ]

    Gene ID: 54896, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SLC66A1provided by HGNC
    Official Full Name
    solute carrier family 66 member 1provided by HGNC
    Primary source
    HGNC:HGNC:26001
    See related
    Ensembl:ENSG00000040487 MIM:614760; AllianceGenome:HGNC:26001
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LAAT1; PQLC2; LAAT-1
    Summary
    Enables L-arginine transmembrane transporter activity and L-lysine transmembrane transporter activity. Involved in L-arginine transmembrane transport; amino acid homeostasis; and lysine transport. Located in lysosomal membrane. Is integral component of organelle membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 2.3), adrenal (RPKM 1.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p36.13
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (19312326..19334463)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (19135861..19158016)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (19638820..19658922)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903867 Neighboring gene uncharacterized LOC100506730 Neighboring gene RNA, U6 small nuclear 1099, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19638229-19638728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19641943-19642442 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:19644916-19645106 Neighboring gene aldo-keto reductase family 7 member A2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19661163-19661664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19661665-19662164 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19663848-19664812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19665979-19666480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19667246-19668220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 299 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19679737-19680421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19682496-19682996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19682997-19683497 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1531 Neighboring gene capping actin protein of muscle Z-line subunit beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19685462-19685962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19696541-19697233 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 301 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:19727675-19728354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19729033-19729710 Neighboring gene uncharacterized LOC124903868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19745938-19746438 Neighboring gene RNA, 7SL, cytoplasmic 277, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Cationic amino acid transporter PQLC2 is a potential therapeutic target in gastric cancer. Jeung YJ, et al. Cancer Sci, 2019 Apr. PMID 30729615, Free PMC Article
    2. Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids. Talaia G, et al. Proc Natl Acad Sci U S A, 2021 Feb 23. PMID 33597295, Free PMC Article
    3. LAAT-1 is the lysosomal lysine/arginine transporter that maintains amino acid homeostasis. Liu B, et al. Science, 2012 Jul 20. PMID 22822152, Free PMC Article
    4. Heptahelical protein PQLC2 is a lysosomal cationic amino acid exporter underlying the action of cysteamine in cystinosis therapy. Jézégou A, et al. Proc Natl Acad Sci U S A, 2012 Dec 11. PMID 23169667, Free PMC Article
    5. A germline-specific class of small RNAs binds mammalian Piwi proteins. Girard A, et al. Nature, 2006 Jul 13. PMID 16751776

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids.
      Title: Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids.
    2. knockdown caused growth arrest and cell death of cancer cells and suppressed tumor growth in a mouse xenograft model. These results suggest that targeting PQLC2 is an effective strategy for GC treatment.
      Title: Cationic amino acid transporter PQLC2 is a potential therapeutic target in gastric cancer.
    3. PQLC2 and Ypq1-3 proteins are lysosomal/vacuolar exporters of CAAs and suggest that small-molecule transport is a conserved feature of the PQ-loop protein family
      Title: Heptahelical protein PQLC2 is a lysosomal cationic amino acid exporter underlying the action of cysteamine in cystinosis therapy.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20320, FLJ23906, FLJ26661, FLJ26665

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-arginine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables L-lysine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables L-lysine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables basic amino acid transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables basic amino acid transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in L-arginine transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in L-lysine transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular amino acid homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in lysine transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transmembrane transport TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in organelle membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lysosomal amino acid transporter 1 homolog
    Names
    PQ loop repeat containing 2
    PQ-loop repeat-containing protein 2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001040125.2 → NP_001035214.1  lysosomal amino acid transporter 1 homolog isoform 1

      See identical proteins and their annotated locations for NP_001035214.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK125580, BC015324, DA202894, DA560373
      Consensus CDS
      CCDS195.2
      UniProtKB/Swiss-Prot
      B3KWQ5, Q6ZMJ3, Q6ZP27, Q6ZP29, Q9NXC7
      Related
      ENSP00000364295.3, ENST00000375153.8
      Conserved Domains (1) summary
      pfam04193
      Location:183 → 238
      PQ-loop; PQ loop repeat

    2. NM_001040126.2 → NP_001035215.1  lysosomal amino acid transporter 1 homolog isoform 2

      See identical proteins and their annotated locations for NP_001035215.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate segment in the 5' UTR and an alternate exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      BC015324, DA202894
      Consensus CDS
      CCDS30618.1
      UniProtKB/TrEMBL
      A0A024RAA1
      Related
      ENSP00000383395.2, ENST00000400548.6
      Conserved Domains (1) summary
      pfam04193
      Location:119 → 173
      PQ-loop; PQ loop repeat

    3. NM_001287531.2 → NP_001274460.1  lysosomal amino acid transporter 1 homolog isoform 3 precursor

      See identical proteins and their annotated locations for NP_001274460.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate segment in the 5' UTR, an alternate exon, and uses an alternate splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK172745, BC015324, DA202894
      UniProtKB/Swiss-Prot
      Q6ZP29
      Conserved Domains (1) summary
      pfam04193
      Location:73 → 127
      PQ-loop; PQ loop repeat

    4. NM_017765.3 → NP_060235.2  lysosomal amino acid transporter 1 homolog isoform 1

      See identical proteins and their annotated locations for NP_060235.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate segment in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (1).
      Source sequence(s)
      AK125580, AK130171, BC015324, DA202894
      Consensus CDS
      CCDS195.2
      UniProtKB/Swiss-Prot
      B3KWQ5, Q6ZMJ3, Q6ZP27, Q6ZP29, Q9NXC7
      Related
      ENSP00000364297.3, ENST00000375155.7
      Conserved Domains (1) summary
      pfam04193
      Location:183 → 238
      PQ-loop; PQ loop repeat

    RNA

    1. NR_109848.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses an alternate 3' exon structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK000327, AL035413

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      19312326..19334463
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423401.1 → XP_047279357.1  lysosomal amino acid transporter 1 homolog isoform X3

    2. XM_011541634.4 → XP_011539936.1  lysosomal amino acid transporter 1 homolog isoform X3

      Conserved Domains (1) summary
      pfam04193
      Location:38 → 97
      PQ-loop; PQ loop repeat

    3. XM_005245916.3 → XP_005245973.1  lysosomal amino acid transporter 1 homolog isoform X2

      See identical proteins and their annotated locations for XP_005245973.1

      UniProtKB/Swiss-Prot
      B3KWQ5, Q6ZMJ3, Q6ZP27, Q6ZP29, Q9NXC7
      Conserved Domains (1) summary
      pfam04193
      Location:183 → 238
      PQ-loop; PQ loop repeat

    4. XM_047423394.1 → XP_047279350.1  lysosomal amino acid transporter 1 homolog isoform X1

    RNA

    1. XR_001737253.2 RNA Sequence

    2. XR_001737254.2 RNA Sequence

    3. XR_007061310.1 RNA Sequence

    4. XR_007061311.1 RNA Sequence

    5. XR_007061312.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      19135861..19158016
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337249.1 → XP_054193224.1  lysosomal amino acid transporter 1 homolog isoform X3

    2. XM_054337250.1 → XP_054193225.1  lysosomal amino acid transporter 1 homolog isoform X3

    3. XM_054337248.1 → XP_054193223.1  lysosomal amino acid transporter 1 homolog isoform X2

      UniProtKB/Swiss-Prot
      B3KWQ5, Q6ZMJ3, Q6ZP27, Q6ZP29, Q9NXC7

    4. XM_054337247.1 → XP_054193222.1  lysosomal amino acid transporter 1 homolog isoform X1

    RNA

    1. XR_008486077.1 RNA Sequence

    2. XR_008486079.1 RNA Sequence

    3. XR_008486076.1 RNA Sequence

    4. XR_008486078.1 RNA Sequence

    5. XR_008486080.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZP29.1 GenPept UniProtKB/Swiss-Prot:Q6ZP29

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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